Merge branch 'master' into appveyor

CMakeLists.txt

@@ -88,6 +88,7 @@ SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/"
 # auto-configure style checks, other CMake modules.
 INCLUDE(${CMAKE_ROOT}/Modules/CheckLibraryExists.cmake)
 INCLUDE(${CMAKE_ROOT}/Modules/CheckIncludeFile.cmake)
+INCLUDE(${CMAKE_ROOT}/Modules/CheckIncludeFiles.cmake)
 INCLUDE(${CMAKE_ROOT}/Modules/CheckTypeSize.cmake)
 INCLUDE(${CMAKE_ROOT}/Modules/CheckFunctionExists.cmake)
 INCLUDE(${CMAKE_ROOT}/Modules/CheckCXXSourceCompiles.cmake)
@@ -333,24 +334,15 @@ OPTION (ENABLE_V2_API "Build netCDF Version 2." ON)
 SET(BUILD_V2 ${ENABLE_V2_API})
 IF(NOT ENABLE_V2_API)
   SET(NO_NETCDF_2 ON)
-ENDIF()
+ELSE(NOT ENABLE_V2_API)
+  SET(USE_NETCDF_2 TRUE)
+ENDIF(NOT ENABLE_V2_API)
 
 # Option to build utilities
 OPTION(BUILD_UTILITIES "Build ncgen, ncgen3, ncdump." ON)
 
 # Option to use MMAP
-OPTION(ENABLE_MMAP "Use MMAP." OFF)
-IF(ENABLE_MMAP)
-  CHECK_FUNCTION_EXISTS(mremap  HAVE_MREMAP)
-  IF(NOT HAVE_MREMAP)
-    MESSAGE(WARNING "mremap not found: disabling MMAP support.")
-    SET(ENABLE_MMAP OFF)
-  ELSE()
-    SET(HAVE_MMAP ON)
-    SET(BUILD_MMAP ON)
-    SET(USE_MMAP ON)
-  ENDIF()
-ENDIF()
+OPTION(ENABLE_MMAP "Use MMAP." ON)
 
 # Option to use examples.
 OPTION(ENABLE_EXAMPLES "Build Examples" ON)
@@ -635,6 +627,9 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
       ENDIF()
 
     ENDIF(MSVC)
+    IF(NOT HDF5_C_LIBRARY)
+      SET(HDF5_C_LIBRARY hdf5)
+    ENDIF()
   ENDIF(HDF5_C_LIBRARY AND HDF5_HL_LIBRARY AND HDF5_INCLUDE_DIR)
 
   ###
@@ -644,29 +639,35 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
     # Find out if HDF5 was built with parallel support.
     # Do that by checking for the targets H5Pget_fapl_mpiposx and
     # H5Pget_fapl_mpio in ${HDF5_LIB}.
-    CHECK_LIBRARY_EXISTS(hdf5 H5Pget_fapl_mpiposix "" HDF5_IS_PARALLEL_MPIPOSIX)
-    CHECK_LIBRARY_EXISTS(hdf5 H5Pget_fapl_mpio "" HDF5_IS_PARALLEL_MPIO)
+    CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5Pget_fapl_mpiposix "" HDF5_IS_PARALLEL_MPIPOSIX)
+    CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5Pget_fapl_mpio "" HDF5_IS_PARALLEL_MPIO)
     IF(HDF5_IS_PARALLEL_MPIPOSIX OR HDF5_IS_PARALLEL_MPIO)
       SET(HDF5_PARALLEL ON)
     ELSE()
       SET(HDF5_PARALLEL OFF)
     ENDIF()
 
     IF(HDF5_IS_PARALLEL_MPIO)
+      SET(HAVE_H5PGET_FAPL_MPIO TRUE)
       SET(USE_PARALLEL_MPIO ON)
     ENDIF()
 
     IF(HDF5_IS_PARALLEL_MPIPOSIX)
       SET(USE_PARALLEL_POSIX ON)
     ENDIF()
 
+    #Check to see if HDF5 library has collective metadata APIs, (HDF5 >= 1.10.0)
+    CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5Pset_all_coll_metadata_ops "" HDF5_HAS_COLL_METADATA_OPS)
+
     OPTION(ENABLE_DYNAMIC_LOADING "Enable Dynamic Loading" ON)
     IF(ENABLE_DYNAMIC_LOADING)
       SET(USE_LIBDL ON CACHE BOOL "")
     ENDIF()
-    SET(HDF5_C_LIBRARY hdf5)
   ENDIF(NOT MSVC)
 
+  # Make sure the user has built the library with zlib support.
+  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5Pset_deflate "" HAVE_H5PSET_DEFLATE)
+
   #Check to see if H5Z_SZIP exists in HDF5_Libraries. If so, we must use szip.
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5P_SZIP "" USE_SZIP)
   IF(USE_SZIP)
@@ -680,8 +681,15 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
   ENDIF()
 
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5free_memory "" HDF5_HAS_H5FREE)
+  IF(HDF5_HAS_H5FREE)
+    SET(HAVE_H5FREE_MEMORY TRUE)
+  ENDIF(HDF5_HAS_H5FREE)
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5Pset_libver_bounds "" HDF5_HAS_LIBVER_BOUNDS)
 
+  IF(HDF5_HAS_LIBVER_BOUNDS)
+    SET(HAVE_H5PSET_LIBVER_BOUNDS TRUE)
+  ENDIF(HDF5_HAS_LIBVER_BOUNDS)
+
   IF(HDF5_PARALLEL)
 	SET(HDF5_CC h5pcc)
   ELSE()
@@ -719,6 +727,14 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
   SET(USE_ZLIB ON)
   INCLUDE_DIRECTORIES(${ZLIB_INCLUDE_DIRS})
 
+  FIND_PATH(HAVE_HDF5_H hdf5.h)
+  IF(NOT HAVE_HDF5_H)
+    MESSAGE(FATAL_ERROR "Compiling a test with hdf5 failed. Either hdf5.h cannot be found, or the log messages should be checked for another reason.")
+  ELSE(NOT HAVE_HDF5_H)
+    INCLUDE_DIRECTORIES(${HAVE_HDF5_H})
+  ENDIF(NOT HAVE_HDF5_H)
+
+
 ENDIF(USE_HDF5 OR ENABLE_NETCDF_4)
 
 
@@ -1115,7 +1131,7 @@ CHECK_INCLUDE_FILE("errno.h"   HAVE_ERRNO_H)
 CHECK_INCLUDE_FILE("fcntl.h"   HAVE_FCNTL_H)
 CHECK_INCLUDE_FILE("getopt.h"  HAVE_GETOPT_H)
 CHECK_INCLUDE_FILE("stdbool.h"   HAVE_STDBOOL_H)
-CHECK_INCLUDE_FILE("locale.h"  HAVE_LOCAL_H)
+CHECK_INCLUDE_FILE("locale.h"  HAVE_LOCALE_H)
 CHECK_INCLUDE_FILE("stdint.h"  HAVE_STDINT_H)
 CHECK_INCLUDE_FILE("stdio.h"   HAVE_STDIO_H)
 CHECK_INCLUDE_FILE("stdlib.h"  HAVE_STDLIB_H)
@@ -1129,27 +1145,87 @@ CHECK_INCLUDE_FILE("sys/stat.h"  HAVE_SYS_STAT_H)
 CHECK_INCLUDE_FILE("sys/time.h"  HAVE_SYS_TIME_H)
 CHECK_INCLUDE_FILE("sys/types.h" HAVE_SYS_TYPES_H)
 CHECK_INCLUDE_FILE("sys/wait.h"  HAVE_SYS_WAIT_H)
+CHECK_INCLUDE_FILE("sys/mman.h"  HAVE_SYS_MMAN_H)
 CHECK_INCLUDE_FILE("sys/resource.h" HAVE_SYS_RESOURCE_H)
 CHECK_INCLUDE_FILE("fcntl.h"  HAVE_FCNTL_H)
 CHECK_INCLUDE_FILE("inttypes.h"  HAVE_INTTYPES_H)
 CHECK_INCLUDE_FILE("pstdint.h"  HAVE_PSTDINT_H)
 CHECK_INCLUDE_FILE("endian.h" HAVE_ENDIAN_H)
 CHECK_INCLUDE_FILE("BaseTsd.h"  HAVE_BASETSD_H)
 CHECK_INCLUDE_FILE("stddef.h"   HAVE_STDDEF_H)
+CHECK_INCLUDE_FILE("memory.h"  HAVE_MEMORY_H)
+CHECK_INCLUDE_FILE("string.h"  HAVE_STRING_H)
+
+CHECK_INCLUDE_FILES("time.h;sys/time.h" TIME_WITH_SYS_TIME)
+
+IF(NOT HAVE_STDLIB_H)
+  SET(NO_STDLIB_H TRUE)
+ENDIF(NOT HAVE_STDLIB_H)
+
+IF(NOT HAVE_SYS_TYPES_H)
+  SET(NO_SYS_TYPES_H TRUE)
+ENDIF(NOT HAVE_SYS_TYPES_H)
+
+
+# Symbol Exists
+CHECK_SYMBOL_EXISTS(isfinite "math.h" HAVE_DECL_ISFINITE)
+CHECK_SYMBOL_EXISTS(isnan "math.h" HAVE_DECL_ISNAN)
+CHECK_SYMBOL_EXISTS(isinf "math.h" HAVE_DECL_ISINF)
+CHECK_SYMBOL_EXISTS(signbit "math.h" HAVE_DECL_SIGNBIT)
+CHECK_SYMBOL_EXISTS(st_blksize "sys/stat.h" HAVE_STRUCT_STAT_ST_BLKSIZE)
+CHECK_SYMBOL_EXISTS(alloca "alloca.h" HAVE_ALLOCA)
+CHECK_SYMBOL_EXISTS(snprintf "stdio.h" HAVE_SNPRINTF)
+CHECK_SYMBOL_EXISTS(vprintf "stdio.h" HAVE_VPRINTF)
+
+# For historic purposes...
+SET(HAVE_ST_BLKSIZE ${HAVE_STRUCT_STAT_ST_BLKSIZE})
 
 # Type checks
 CHECK_TYPE_SIZE("void*"     SIZEOF_VOIDSTAR)
 CHECK_TYPE_SIZE("char"      SIZEOF_CHAR)
 CHECK_TYPE_SIZE("double"    SIZEOF_DOUBLE)
 CHECK_TYPE_SIZE("float"     SIZEOF_FLOAT)
 CHECK_TYPE_SIZE("int"       SIZEOF_INT)
+CHECK_TYPE_SIZE("uint"      SIZEOF_UINT)
+IF(SIZEOF_UINT)
+  SET(HAVE_UINT TRUE)
+ENDIF(SIZEOF_UINT)
+
 CHECK_TYPE_SIZE("long"      SIZEOF_LONG)
 CHECK_TYPE_SIZE("long long" SIZEOF_LONG_LONG)
+IF(SIZEOF_LONG_LONG)
+  SET(HAVE_LONG_LONG_INT TRUE)
+ENDIF(SIZEOF_LONG_LONG)
+
+CHECK_TYPE_SIZE("unsigned long long" SIZEOF_UNSIGNED_LONG_LONG)
+IF(SIZEOF_UNSIGNED_LONG_LONG)
+  SET(HAVE_UNSIGNED_LONG_LONG_INT TRUE)
+ENDIF(SIZEOF_UNSIGNED_LONG_LONG)
+
 CHECK_TYPE_SIZE("off_t"     SIZEOF_OFF_T)
 CHECK_TYPE_SIZE("off64_t"   SIZEOF_OFF64_T)
 CHECK_TYPE_SIZE("short"     SIZEOF_SHORT)
+CHECK_TYPE_SIZE("ushort"    SIZEOF_USHORT)
+IF(SIZEOF_USHORT)
+  SET(HAVE_USHORT TRUE)
+ENDIF(SIZEOF_USHORT)
+
+CHECK_TYPE_SIZE("_Bool"     SIZEOF__BOOL)
+IF(SIZEOF__BOOL)
+  SET(HAVE__BOOL TRUE)
+ENDIF(SIZEOF__BOOL)
+
 CHECK_TYPE_SIZE("size_t"    SIZEOF_SIZE_T)
+IF(SIZEOF_SIZE_T)
+  SET(HAVE_SIZE_T TRUE)
+ENDIF(SIZEOF_SIZE_T)
+
 CHECK_TYPE_SIZE("ssize_t"   SIZEOF_SSIZE_T)
+CHECK_TYPE_SIZE("ptrdiff_t" SIZEOF_PTRDIFF_T)
+IF(SIZEOF_PTRDIFF_T)
+  SET(HAVE_PTRDIFF_T TRUE)
+ENDIF(SIZEOF_PTRDIFF_T)
+
 # __int64 is used on Windows for large file support.
 CHECK_TYPE_SIZE("__int64"   SIZEOF___INT_64)
 CHECK_TYPE_SIZE("uchar"     SIZEOF_UCHAR)
@@ -1176,7 +1252,6 @@ ENDIF()
 CHECK_FUNCTION_EXISTS(fsync HAVE_FSYNC)
 CHECK_FUNCTION_EXISTS(strlcat   HAVE_STRLCAT)
 CHECK_FUNCTION_EXISTS(strerror  HAVE_STRERROR)
-CHECK_FUNCTION_EXISTS(snprintf  HAVE_SNPRINTF)
 CHECK_FUNCTION_EXISTS(strchr  HAVE_STRCHR)
 CHECK_FUNCTION_EXISTS(strrchr HAVE_STRRCHR)
 CHECK_FUNCTION_EXISTS(strcat  HAVE_STRCAT)
@@ -1186,20 +1261,35 @@ CHECK_FUNCTION_EXISTS(strndup HAVE_STRNDUP)
 CHECK_FUNCTION_EXISTS(strcasecmp  HAVE_STRCASECMP)
 CHECK_FUNCTION_EXISTS(strtod  HAVE_STRTOD)
 CHECK_FUNCTION_EXISTS(strtoll HAVE_STRTOLL)
-CHECK_FUNCTION_EXISTS(strtoull  HAVE_STROULL)
+CHECK_FUNCTION_EXISTS(strtoull  HAVE_STRTOULL)
 CHECK_FUNCTION_EXISTS(strstr  HAVE_STRSTR)
 CHECK_FUNCTION_EXISTS(mkstemp HAVE_MKSTEMP)
 CHECK_FUNCTION_EXISTS(rand  HAVE_RAND)
 CHECK_FUNCTION_EXISTS(random HAVE_RANDOM)
 CHECK_FUNCTION_EXISTS(gettimeofday  HAVE_GETTIMEOFDAY)
 CHECK_FUNCTION_EXISTS(fsync HAVE_FSYNC)
-CHECK_FUNCTION_EXISTS(MPI_Comm_f2C  HAVE_MPI_COMM_F2C)
+CHECK_FUNCTION_EXISTS(MPI_Comm_f2c  HAVE_MPI_COMM_F2C)
 CHECK_FUNCTION_EXISTS(memmove HAVE_MEMMOVE)
+CHECK_FUNCTION_EXISTS(memcmp HAVE_MEMCMP)
 CHECK_FUNCTION_EXISTS(getpagesize HAVE_GETPAGESIZE)
 CHECK_FUNCTION_EXISTS(sysconf HAVE_SYSCONF)
 CHECK_FUNCTION_EXISTS(getrlimit HAVE_GETRLIMIT)
 CHECK_FUNCTION_EXISTS(_filelengthi64 HAVE_FILE_LENGTH_I64)
+CHECK_FUNCTION_EXISTS(mmap HAVE_MMAP)
+CHECK_FUNCTION_EXISTS(mremap HAVE_MREMAP)
+
+IF(ENABLE_MMAP)
+  IF(NOT HAVE_MREMAP)
+    MESSAGE(WARNING "mremap not found: disabling MMAP support.")
+    SET(ENABLE_MMAP OFF)
+  ELSE(NOT HAVE_MREMAP)
+    SET(HAVE_MMAP ON)
+    SET(BUILD_MMAP ON)
+    SET(USE_MMAP ON)
+  ENDIF(NOT HAVE_MREMAP)
+ENDIF(ENABLE_MMAP)
 
+#CHECK_FUNCTION_EXISTS(alloca HAVE_ALLOCA)
 #####
 # End system inspection checks.
 #####

RELEASE_NOTES.md

@@ -11,6 +11,8 @@ This file contains a high-level description of this package's evolution. Release
 
 ## 4.4.2 - TBD
 
+* [Enhancement] Added support for HDF5 collective metadata operations when available. Patch submitted by Greg Sjaardema, see [Pull request #335](https://github.com/Unidata/netcdf-c/pull/335) for more information.
+* [Bug] Addressed a potential type punning issue. See [GitHub #351](https://github.com/Unidata/netcdf-c/issues/351) for more information.
 * [Bug] Addressed an issue where netCDF wouldn't build on Windows systems using MSVC 2012. See [GitHub #304](https://github.com/Unidata/netcdf-c/issues/304) for more information.
 * [Bug] Fixed an issue related to potential type punning, see [GitHub #344](https://github.com/Unidata/netcdf-c/issues/344) for more information.
 * [Enhancement] Incorporated an enhancement provided by Greg Sjaardema, which may improve read/write times for some complex files.  Basically, linked lists were replaced in some locations where it was safe to use an array/table.  See [Pull request #328](https://github.com/Unidata/netcdf-c/pull/328) for more information.

cf.cmake

@@ -1,56 +1,23 @@
 # Is netcdf-4 and/or DAP enabled?
-#NC4=1
-#DAP=1
+NC4=1
+DAP=1
 
 # Is visual studio being used?
-#VS=yes
-CYGWIN=yes
+VS=yes
+#CYGWIN=yes
+
 
 if test "x$VS" = x ; then
 #CC=mpicc
 CC=gcc
-fi
-
-export CC
-
-if test "x$VS" != x -a "x$CYGWIN" != x ; then
-  ZLIB=cygz.dll; H5LIB=cyghdf5.dll; H5LIB_HL=cyghdf5_hl.dll; CURLLIB=cygcurl.dll
-elif test "x$VS" = x -a "x$CYGWIN" != x ; then
-  ZLIB=libz.dll.a; H5LIB=libhdf5.dll.a; H5LIB_HL=libhdf5_hl.dll.a; CURLLIB=libcurl.dll.a
-elif test "x$VS" = x -a "x$CYGWIN" == x ; then
-  ZLIB=libz.so; H5LIB=libhdf5.so; H5LIB_HL=libhdf5_hl.so; CURLLIB=libcurl.so
 else
-  echo "cannot determine library names"
-  exit 1
-fi
-
-for p in /usr/bin /usr/local/bin /usr/local/lib /usr/lib ; do
-if test -f $p/$ZLIB ; then ZP=$p; fi
-if test -f $p/$H5LIB ; then HP=$p; fi
-if test -f $p/$CURLLIB ; then CP=$p; fi
-done
-
-if test "x$ZP" = x ; then echo "Cannot find z lib" ; exit 1; fi
-if test "x$HP" = x ; then echo "Cannot find hdf5 lib" ; exit 1; fi
-if test "x$CP" = x ; then echo "Cannot find curl lib" ; exit 1; fi
-
-if test "x$CYGWIN" != x -a "x$VS" != x; then
-ZP=`cygpath -w "$ZP"`
-HP=`cygpath -w "$HP"`
-CP=`cygpath -w "$CP"`
+VSSTRING="Visual Studio 12 2013 Win64"
+G="-G\"$VSSTRING\""
 fi
 
-#if test "x$VS" != x ; then USR=c:/cygwin/usr; else USR=/usr; fi
-
-ZLIB="-DZLIB_LIBRARY=${ZP}/$ZLIB -DZLIB_INCLUDE_DIR=${ZP}/include -DZLIB_INCLUDE_DIRS=${ZP}/include"
-if test "x$NC4" = x1 ; then
-HDF5="-DHDF5_LIB=${HP}/$H5LIB -DHDF5_HL_LIB=${HP}/$H5LIB_HL -DHDF5_INCLUDE_DIR=${HP}/include"
-fi
-if test "x$DAP" = x1 ; then
-CURL="-DCURL_LIBRARY=${CP}/$CURLLIB -DCURL_INCLUDE_DIR=${CP}/include -DCURL_INCLUDE_DIRS=${CP}/include"
-fi
+export CC
 
-#FLAGS="$FLAGS -DCMAKE_C_FLAGS='-Wall -Wno-unused-but-set-variable -Wno-unused-variable -Wno-unused-parameter'"x2
+FLAGS="-DCMAKE_PREFIX_PATH=c:/tools/nccmake"
 
 if test "x$DAP" = x ; then
 FLAGS="$FLAGS -DENABLE_DAP=false"
@@ -59,17 +26,13 @@ if test "x$NC4" = x ; then
 FLAGS="$FLAGS -DENABLE_NETCDF_4=false"
 fi
 FLAGS="$FLAGS -DENABLE_CONVERSION_WARNINGS=false"
-
-FLAGS="$FLAGS -DCMAKE_INSTALL_PREFIX=$USR/local"
-#FLAGS="-DCMAKE_PREFIX_PATH=$PPATH"
-#FLAGS="$FLAGS -DCMAKE_PREFIX_PATH=$PPATH"
 FLAGS="$FLAGS -DENABLE_DAP_REMOTE_TESTS=true"
-#FLAGS="$FLAGS -DENABLE_DAP_AUTH_TESTS=true"
+FLAGS="$FLAGS -DENABLE_TESTS=true"
 
 rm -fr build
 mkdir build
 cd build
 
-cmake $FLAGS ${ZLIB} ${HDF5} ${CURL} ..
-cmake --build .
+cmake -GVisual\ Studio\ 14\ 2015 $FLAGS ${ZLIB} ${HDF5} ${CURL} ..
+#cmake --build .
 CTEST_OUTPUT_ON_FAILURE=1 cmake --build . --target test